This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This is a NIH sponsored, multi-center protocol. Hypothesis: Minocycline treatment for 24 weeks will improve HIV-associated cognitive impairment and will be safe and well-tolerated. Primary Objective: To examine whether minocycline treatment for 24 weeks improves HIV-associated cognitive impairment. Secondary Objectives: To examine whether minocycline treatment for 24 weeks is safe and well-tolerated in individuals with HIV-associated cognitive impairment. To examine whether minocycline treatment for 48 weeks is safe and well-tolerated in individuals with HIV-associated cognitive impairment. To examine whether minocycline treatment for 24 weeks improves functional impairment. To examine whether minocycline treatment for 24 weeks decreases levels of several markers of HIV-associated cognitive impairment including, but not limited to, HIV-1 RNA;a marker of immune activation, [monocyte chemoattractant protein (MCP-1)];a marker of apoptosis (sFas);markers of oxidative stress [ceramide, sphingomyelin, 4-hydroxynonenal (HNE), and 3-nitrotyrosine [3-NT] modified proteins] in blood and cerebrospinal fluid (CSF). To examine whether minocycline decreases the plasma concentration of atazanavir.